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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ) $local_species = 'aag' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ) $local_species = 'can' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ) $local_species = 'cde' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ) $local_species = 'mco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ) $local_species = 'pso' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ) $local_species = 'pax' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ) $local_species = 'ppa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ) $local_species = 'pco' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ) $local_species = 'smo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ), 'gf_id' => 'HOM05D001154', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001154' ), 'data_identifier' => 'HOM05D001154', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001154', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '535', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p21980' => 'bna', 'A03p42300' => 'bna', 'A03p49180' => 'bna', 'A10p26370' => 'bna', 'Aa31LG3G15820' => 'aar', 'Aa31LG8G8180' => 'aar', 'Aa31LG9G1870' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.2438' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_228.1483' => 'aag', 'Actinidia06507' => 'ach', 'Actinidia14075' => 'ach', 'Actinidia15694' => 'ach', 'Actinidia17329' => 'ach', 'Actinidia23442' => 'ach', 'Actinidia38615' => 'ach', 'Actinidia38646' => 'ach', 'Ah.03g139820' => 'amhyb', 'Ah.04g154030' => 'amhyb', 'Ah.12g063770' => 'amhyb', 'AL3G35610' => 'aly', 'AL6G22020' => 'aly', 'AL7G39950' => 'aly', 'Aqoxy2G03152' => 'aox', 'Aqoxy4G01849' => 'aox', 'Aqoxy6G00826' => 'aox', 'Aqoxy7G02022' => 'aox', 'arahy.Tifrunner.gnm1.ann1.00UVWE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.1181X5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.26PQ7F' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.3I7KH6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.4MIV3X' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.6UIE9D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.96HG27' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DSI4M6' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E471WB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E4EAWN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E5IAKT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.I8UD53' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IE214W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.RRZ6LI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UN6GTT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UQP6RN' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VHR0A7' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.VLP716' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z8U3KU' => 'arhy', 'AT3G21500' => 'ath', 'AT4G15560' => 'ath', 'AT5G11380' => 'ath', 'ATR0580G266' => 'atr', 'ATR0580G454' => 'atr', 'ATR0706G160' => 'atr', 'ATR0716G058' => 'atr', 'ATR0767G264' => 'atr', 'Atru.chr10.548' => 'acertr', 'Atru.chr3.1219' => 'acertr', 'Atru.chr3.648' => 'acertr', 'Atru.chr3.694' => 'acertr', 'Atru.chr3.695' => 'acertr', 'Atru.chr4.2723' => 'acertr', 'Atru.chr7.2365' => 'acertr', 'Atru.chr7.581' => 'acertr', 'AUR62003680' => 'cqu', 'AUR62017990' => 'cqu', 'AUR62032345' => 'cqu', 'AUR62033631' => 'cqu', 'AUR62040729' => 'cqu', 'AUR62041840' => 'cqu', 'BcaB04g19170' => 'bca', 'BcaB04g20585' => 'bca', 'BcaB08g37067' => 'bca', 'BcaC01g03500' => 'bca', 'BcaC04g19236' => 'bca', 'BcaC06g32943' => 'bca', 'BcaC06g33417' => 'bca', 'BcaC09g50254' => 'bca', 'BcaNung00262' => 'bca', 'BolC1t02677H' => 'bol', 'BolC3t17459H' => 'bol', 'BolC7t45246H' => 'bol', 'BolC9t59375H' => 'bol', 'BraA01t02104Z' => 'bra', 'BraA03t13381Z' => 'bra', 'BraA03t14013Z' => 'bra', 'BraA10t44694Z' => 'bra', 'C01p27370' => 'bna', 'C03p51750' => 'bna', 'C07p47230' => 'bna', 'C09p65510' => 'bna', 'CAN.G1771.8' => 'can', 'CAN.G185.11' => 'can', 'CAN.G98.9' => 'can', 'CANSAT01G2171' => 'cansat', 'CANSAT11G1124' => 'cansat', 'CANSAT78G0190' => 'cansat', 'CARHR201880' => 'chi', 'CARHR289970' => 'chi', 'Carub.0003s2154' => 'cru', 'Carub.0006s0982' => 'cru', 'Carub.0007s2628' => 'cru', 'Ca_13457_v3' => 'car', 'Ca_13458_v3' => 'car', 'Ca_13459_v3' => 'car', 'Ca_15713_v3' => 'car', 'Ca_21556_v3' => 'car', 'Ca_22622_v3' => 'car', 'Ca_22962_v3' => 'car', 'CBR_g3582' => 'cbr', 'Cc03_g02540' => 'ccan', 'Cc06_g13680' => 'ccan', 'Cc07_g13880' => 'ccan', 'Cc11_g01700' => 'ccan', 'CDE02G1615' => 'cde', 'CDE02G2634' => 'cde', 'CDE02G2786' => 'cde', 'CDE02G4100' => 'cde', 'CDE05G2299' => 'cde', 'CDE05G3144' => 'cde', 'Cfa006865' => 'cfa', 'Cfa013188' => 'cfa', 'Cfa013528' => 'cfa', 'Cfa015515' => 'cfa', 'Ciclev10004432m.g' => 'ccl', 'Ciclev10007595m.g' => 'ccl', 'Ciclev10009166m.g' => 'ccl', 'Ciclev10024949m.g' => 'ccl', 'CiPaw.01G155100' => 'cil', 'CiPaw.02G087800' => 'cil', 'CiPaw.07G045900' => 'cil', 'CiPaw.07G188800' => 'cil', 'CiPaw.07G220000' => 'cil', 'ClCG06G005530' => 'cla', 'ClCG06G013090' => 'cla', 'ClCG08G013060' => 'cla', 'ClCG10G007830' => 'cla', 'ClCG10G007840' => 'cla', 'COL.COLO4_19551' => 'col', 'COL.COLO4_23994' => 'col', 'COL.COLO4_27375' => 'col', 'Cpa.g.sc16.90' => 'cpa', 'Cpa.g.sc55.8' => 'cpa', 'Cpa.g.sc91.36' => 'cpa', 'Cre07.g356350' => 'cre', 'CsaV3_1G031250' => 'csa', 'CsaV3_2G031800' => 'csa', 'CsaV3_3G006930' => 'csa', 'CsaV3_6G005620' => 'csa', 'CSS0005962' => 'camsi', 'CSS0018056' => 'camsi', 'CSS0020259' => 'camsi', 'CSS0020368' => 'camsi', 'CSS0023867' => 'camsi', 'CSS0032831' => 'camsi', 'CSS0040369' => 'camsi', 'DCAR_009911' => 'dca', 'DCAR_014178' => 'dca', 'DCAR_022887' => 'dca', 'DCAR_030576' => 'dca', 'Dinv13567' => 'din', 'Dinv30184' => 'din', 'Dinv36952' => 'din', 'Dinv38339' => 'din', 'Dinv41281' => 'din', 'Dinv44440' => 'din', 'Duzib147G1307' => 'dzi', 'Duzib150G1203' => 'dzi', 'Duzib151G0652' => 'dzi', 'Duzib168G1863' => 'dzi', 'Duzib170G0578' => 'dzi', 'Duzib187G1665' => 'dzi', 'Duzib212G0423' => 'dzi', 'ECA240G0040' => 'eca', 'ECA240G0579' => 'eca', 'ECA240G0751' => 'eca', 'ECA240G1345' => 'eca', 'ECA246G3245' => 'eca', 'ECA246G5210' => 'eca', 'EL10Ac2g02576' => 'bvu', 'EL10Ac3g06524' => 'bvu', 'EL10Ac6g15182' => 'bvu', 'Eucgr.C01793' => 'egr', 'Eucgr.H03664' => 'egr', 'Eucgr.I00566' => 'egr', 'FAN07G1730' => 'fan', 'FAN07G1754' => 'fan', 'FAN12G1219' => 'fan', 'FAN12G3845' => 'fan', 'FAN15G2564' => 'fan', 'FAN17G0838' => 'fan', 'FAN19G0224' => 'fan', 'FAN19G2277' => 'fan', 'FAN20G1213' => 'fan', 'FAN22G0810' => 'fan', 'FAN23G0927' => 'fan', 'FAN24G2115' => 'fan', 'FAN26G1564' => 'fan', 'FAN27G0584' => 'fan', 'FAN28G2545' => 'fan', 'FvH4_1g19340' => 'fve', 'FvH4_2g29720' => 'fve', 'FvH4_4g16950' => 'fve', 'Glyma.04G069600' => 'gma', 'Glyma.06G071300' => 'gma', 'Glyma.07G252600' => 'gma', 'Glyma.08G277000' => 'gma', 'Glyma.08G277100' => 'gma', 'Glyma.09G200500' => 'gma', 'Glyma.13G093866' => 'gma', 'Glyma.13G093932' => 'gma', 'Glyma.13G213500' => 'gma', 'Glyma.15G099300' => 'gma', 'Glyma.17G021800' => 'gma', 'Glyma.17G066500' => 'gma', 'Glyma.18G148700' => 'gma', 'Gohir.A08G022100' => 'ghi', 'Gohir.A08G022500' => 'ghi', 'Gohir.A08G022600' => 'ghi', 'Gohir.A08G090186' => 'ghi', 'Gohir.A10G102486' => 'ghi', 'Gohir.A12G069550' => 'ghi', 'Gohir.A12G085500' => 'ghi', 'Gohir.D08G032700' => 'ghi', 'Gohir.D08G033100' => 'ghi', 'Gohir.D08G033300' => 'ghi', 'Gohir.D08G103801' => 'ghi', 'Gohir.D10G165100' => 'ghi', 'Gohir.D12G083600' => 'ghi', 'Gorai.004G030400' => 'gra', 'Gorai.004G030800' => 'gra', 'Gorai.004G030900' => 'gra', 'Gorai.004G111100' => 'gra', 'Gorai.008G093600' => 'gra', 'Gorai.011G184200' => 'gra', 'GSVIVG01003955001' => 'vvi', 'GSVIVG01013194001' => 'vvi', 'GSVIVG01016842001' => 'vvi', 'GSVIVG01017832001' => 'vvi', 'GSVIVG01029109001' => 'vvi', 'GSVIVG01029112001' => 'vvi', 'GSVIVG01029169001' => 'vvi', 'GSVIVG01035799001' => 'vvi', 'HanXRQChr03g0062771' => 'han', 'HanXRQChr03g0080121' => 'han', 'HanXRQChr10g0303851' => 'han', 'HanXRQChr12g0368961' => 'han', 'HanXRQChr16g0516321' => 'han', 'HanXRQChr16g0516331' => 'han', 'Haze_01036' => 'cav', 'Haze_03898' => 'cav', 'Haze_21581' => 'cav', 'Haze_22134' => 'cav', 'Hma1.2p1_0000F.1_g000870' => 'hma', 'Hma1.2p1_0000F.1_g000880' => 'hma', 'Hma1.2p1_0078F.1_g040890' => 'hma', 'Hma1.2p1_0643F.1_g194660' => 'hma', 'Hma1.2p1_1261F.1_g271160' => 'hma', 'Hma1.2p1_1671F.1_g296730' => 'hma', 'HPP92_013689' => 'vpl', 'HPP92_018833' => 'vpl', 'Hund16520' => 'sun', 'Hund24900' => 'sun', 'Hund25701' => 'sun', 'Hund25702' => 'sun', 'Lalb_Chr05g0216261' => 'lal', 'Lalb_Chr09g0325921' => 'lal', 'Lalb_Chr12g0196411' => 'lal', 'Lalb_Chr16g0381581' => 'lal', 'Lalb_Chr18g0055821' => 'lal', 'Lalb_Chr22g0349481' => 'lal', 'Lalb_Chr23g0268811' => 'lal', 'Lj1g0005701' => 'lja', 'Lj2C527T2' => 'lonja', 'Lj2g0015464' => 'lja', 'Lj3C808G8' => 'lonja', 'Lj3C808T7' => 'lonja', 'Lj4C267T4' => 'lonja', 'Lj4C269T1' => 'lonja', 'Lj4C269T2' => 'lonja', 'Lj4g0016770' => 'lja', 'Lj4g0016916' => 'lja', 'Lj4g0021254' => 'lja', 'Lj4g0026884' => 'lja', 'Lj4P269T15' => 'lonja', 'Lj6g0026045' => 'lja', 'Lj7C716T10' => 'lonja', 'Lj9A133T12' => 'lonja', 'Lj9A690T26' => 'lonja', 'Lj9C690G4' => 'lonja', 'Lj9C735G8' => 'lonja', 'Lju188C5T2' => 'lonja', 'Lju337C2T0' => 'lonja', 'Lju760A3T7' => 'lonja', 'Lju760C3G2' => 'lonja', 'Lsat_1_v5_gn_0_46700' => 'lsa', 'Lsat_1_v5_gn_3_63200' => 'lsa', 'Lsat_1_v5_gn_5_128080' => 'lsa', 'Lsat_1_v5_gn_5_50541' => 'lsa', 'Lsat_1_v5_gn_7_51781' => 'lsa', 'Manes.03G017900' => 'mes', 'Manes.06G028100' => 'mes', 'Manes.12G124300' => 'mes', 'Manes.13G101600' => 'mes', 'Manes.14G161600' => 'mes', 'Manes.15G018800' => 'mes', 'Manes.16G118600' => 'mes', 'Mapoly0015s0196' => 'mpo', 'Mapoly0070s0009' => 'mpo', 'MBI01_g34144_MAGBIO' => 'mbi', 'MBI14_g37767_MAGBIO' => 'mbi', 'MBI16_g00659_MAGBIO' => 'mbi', 'MBI16_g00676_MAGBIO' => 'mbi', 'MBI16_g00677_MAGBIO' => 'mbi', 'MBI16_g00678_MAGBIO' => 'mbi', 'MBI16_g00679_MAGBIO' => 'mbi', 'MBI16_g00680_MAGBIO' => 'mbi', 'MBI16_g06014_MAGBIO' => 'mbi', 'MBI16_g06015_MAGBIO' => 'mbi', 'MBI16_g06016_MAGBIO' => 'mbi', 'MBI19_g27955_MAGBIO' => 'mbi', 'MCO01G530' => 'mco', 'MD01G1041300' => 'mdo', 'MD08G1142600' => 'mdo', 'MD13G1175400' => 'mdo', 'MD15G1119100' => 'mdo', 'MD15G1309900' => 'mdo', 'MD16G1177200' => 'mdo', 'Medtr2g020590' => 'mtr', 'Medtr3g107740' => 'mtr', 'Medtr4g118640' => 'mtr', 'Medtr8g068265' => 'mtr', 'Medtr8g068300' => 'mtr', 'MELO3C011230.2' => 'cme', 'MELO3C014965.2' => 'cme', 'MELO3C014966.2' => 'cme', 'MELO3C017499.2' => 'cme', 'MELO3C021375.2' => 'cme', 'MELO3C029119.2' => 'cme', 'MELO3C029143.2' => 'cme', 'Migut.A00305' => 'egut', 'Migut.A00306' => 'egut', 'Migut.A00322' => 'egut', 'Migut.G00229' => 'egut', 'Migut.H02280' => 'egut', 'Migut.J01446' => 'egut', 'Migut.K01200' => 'egut', 'Migut.M00270' => 'egut', 'MSTRG.10729' => 'ama', 'MSTRG.11760' => 'ama', 'MSTRG.2604' => 'ama', 'MSTRG.2605' => 'ama', 'MSTRG.3961' => 'ama', 'MSTRG.6194' => 'ama', 'Nitab4.5_0000151g0300' => 'nta', 'Nitab4.5_0000402g0040' => 'nta', 'Nitab4.5_0001120g0030' => 'nta', 'Nitab4.5_0003546g0010' => 'nta', 'Nitab4.5_0003813g0010' => 'nta', 'Nitab4.5_0003813g0020' => 'nta', 'Nn2g11920' => 'nnu', 'Nn3g21240' => 'nnu', 'Nn4g26076' => 'nnu', 'Oeu003811.1' => 'oeu', 'Oeu010959.1' => 'oeu', 'Oeu012261.1' => 'oeu', 'Oeu029281.1' => 'oeu', 'Oeu032332.1' => 'oeu', 'Oeu037632.1' => 'oeu', 'Os05g0408900' => 'osa', 'Os06g0142900' => 'osa', 'Os07g0190000' => 'osa', 'Peaxi162Scf00048g02226' => 'pax', 'Peaxi162Scf00085g01215' => 'pax', 'Peaxi162Scf00085g01311' => 'pax', 'Peaxi162Scf00161g00086' => 'pax', 'Peaxi162Scf00359g00066' => 'pax', 'Peaxi162Scf00359g00620' => 'pax', 'Peaxi162Scf00359g00621' => 'pax', 'Peaxi162Scf00797g00034' => 'pax', 'PGR004G0175' => 'pgr', 'PGR031G0836' => 'pgr', 'PGR031G3315' => 'pgr', 'PGSC0003DMG400016120' => 'stu', 'PGSC0003DMG400022855' => 'stu', 'PGSC0003DMG400029091' => 'stu', 'Phvul.003G099600' => 'pvu', 'Phvul.003G148900' => 'pvu', 'Phvul.003G287800' => 'pvu', 'Phvul.003G287900' => 'pvu', 'Phvul.006G159900' => 'pvu', 'Phvul.009G095900' => 'pvu', 'Potri.006G171700' => 'ptr', 'Potri.006G249700' => 'ptr', 'Potri.007G058500' => 'ptr', 'Potri.008G196500' => 'ptr', 'Potri.010G015200' => 'ptr', 'Potri.018G031800' => 'ptr', 'Pp3c11_14460' => 'ppa', 'Pp3c1_11090' => 'ppa', 'Pp3c2_27550' => 'ppa', 'Pp3c7_8920' => 'ppa', 'PRCOL_00004999' => 'pco', 'Prupe.1G144100' => 'ppe', 'Prupe.1G472400' => 'ppe', 'Prupe.6G204700' => 'ppe', 'Psat1g186480' => 'psa', 'Psat1g186560' => 'psa', 'Psat4g029960' => 'psa', 'Psat4g117520' => 'psa', 'Psat4g218120' => 'psa', 'Psat5g027320' => 'psa', 'PSO063G0065' => 'pso', 'PSO170G2215' => 'pso', 'PSO210G2584' => 'pso', 'PSO455G0048' => 'pso', 'PSO455G0090' => 'pso', 'PSO541G3161' => 'pso', 'PSO675G2054' => 'pso', 'PSO832G3123' => 'pso', 'QL02p096727' => 'qlo', 'QL02p096756' => 'qlo', 'QL06p006770' => 'qlo', 'QL06p019913' => 'qlo', 'QL06p036076' => 'qlo', 'QL06p036262' => 'qlo', 'QL12p037888' => 'qlo', 'RcHm_v2.0_Chr2g0110711' => 'rch', 'RcHm_v2.0_Chr4g0403671' => 'rch', 'RcHm_v2.0_Chr4g0403701' => 'rch', 'RcHm_v2.0_Chr4g0420531' => 'rch', 'RcHm_v2.0_Chr6g0298741' => 'rch', 'Rhsim03G0262500' => 'rsi', 'Rhsim04G0214400' => 'rsi', 'Rhsim04G0214500' => 'rsi', 'Sabra06G0132400' => 'sbr', 'Sabra06G0195400' => 'sbr', 'Sabra07G0050000' => 'sbr', 'Sabra10G0009800' => 'sbr', 'SalBow2G0581' => 'sbo', 'SalBow2G0924' => 'sbo', 'SalBow3G4133' => 'sbo', 'SalBow5G3061' => 'sbo', 'SalBow6G3215' => 'sbo', 'SalBow6G4639' => 'sbo', 'SalBow8G2321' => 'sbo', 'SalBow8G2346' => 'sbo', 'Sc03g0000450' => 'sci', 'Sc08g0006240' => 'sci', 'Sc09g0008640' => 'sci', 'Sc13g0003720' => 'sci', 'Sc13g0003730' => 'sci', 'Sc13g0003740' => 'sci', 'Sed0002413' => 'sed', 'Sed0004954' => 'sed', 'Sed0016698' => 'sed', 'Sed0018423' => 'sed', 'Sed0027477' => 'sed', 'SEGI_02083' => 'sgi', 'SEGI_03254' => 'sgi', 'SEGI_12779' => 'sgi', 'SEGI_17913' => 'sgi', 'SEGI_25781' => 'sgi', 'SEGI_30319' => 'sgi', 'SEGI_34813' => 'sgi', 'SGA_v2.0_scaffold195G40869' => 'sas', 'SGA_v2.0_scaffold242G44232' => 'sas', 'SGA_v2.0_scaffold448G51763' => 'sas', 'SGA_v2.0_scaffold66G22482' => 'sas', 'SGA_v2.0_scaffold89G27565' => 'sas', 'SMO165G0014' => 'smo', 'SMO351G0003' => 'smo', 'Solyc01g067890.4' => 'sly', 'Solyc08g066950.3' => 'sly', 'Solyc11g010850.2' => 'sly', 'Sopen01g029840' => 'spe', 'Sopen08g020910' => 'spe', 'Sopen11g005620' => 'spe', 'Sp3g19540' => 'spa', 'Sp6g32220' => 'spa', 'Sp7g13820' => 'spa', 'TAR362G1321' => 'tar', 'TAR365G1041' => 'tar', 'TAR365G1222' => 'tar', 'TAR371G0483' => 'tar', 'TAR381G1621' => 'tar', 'TAR383G0622' => 'tar', 'TAR625G1267' => 'tar', 'TAR626G1098' => 'tar', 'TAR628G0333' => 'tar', 'TAR629G2495' => 'tar', 'TAR686G0001' => 'tar', 'TAR686G0003' => 'tar', 'THA.LOC104799226' => 'tha', 'THA.LOC104802565' => 'tha', 'THA.LOC104820232' => 'tha', 'THA.LOC104821763' => 'tha', 'Thecc.01G088400' => 'tca', 'Thecc.01G088500' => 'tca', 'Thecc.04G274800' => 'tca', 'Thecc.09G148200' => 'tca', 'Thecc.09G165600' => 'tca', 'Thhalv10012843m.g' => 'esa', 'Thhalv10020205m.g' => 'esa', 'Thhalv10024542m.g' => 'esa', 'TPR.G12097' => 'tpr', 'TPR.G14958' => 'tpr', 'TPR.G1504' => 'tpr', 'TPR.G19080' => 'tpr', 'TPR.G25773' => 'tpr', 'TPR.G28555' => 'tpr', 'TWI09G0625' => 'twi', 'TWI34G1766' => 'twi', 'TWI34G1780' => 'twi', 'TWI53G1461' => 'twi', 'TWI53G1888' => 'twi', 'TWI74G0035' => 'twi', 'TWI77G0386' => 'twi', 'unitig_32.g10928' => 'ugi', 'unitig_62.g23466' => 'ugi', 'unitig_62.g23467' => 'ugi', 'unitig_699.g19991' => 'ugi', 'unitig_699.g19992' => 'ugi', 'vmacro05199' => 'vma', 'vmacro06033' => 'vma', 'vmacro06034' => 'vma', 'vmacro08223' => 'vma', 'vmacro08224' => 'vma', 'vmacro13020' => 'vma', 'VMungo0251G0842' => 'vmu', 'VMungo0540G2391' => 'vmu', 'VMungo1000G0001' => 'vmu', 'VMungo1215G2736' => 'vmu', 'VMungo1215G2834' => 'vmu', 'VMungo1309G2961' => 'vmu', 'Zm00001eb287860' => 'zma', 'Zm00001eb302370' => 'zma', 'Zm00001eb377300' => 'zma' ) $gf_id = 'HOM05D001154' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001154' ) $data_identifier = 'HOM05D001154' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 8, 'aar' => (int) 3, 'aag' => (int) 2, 'ach' => (int) 7, 'amhyb' => (int) 3, 'aly' => (int) 3, 'aox' => (int) 4, 'arhy' => (int) 19, 'ath' => (int) 3, 'atr' => (int) 5, 'acertr' => (int) 8, 'cqu' => (int) 6, 'bca' => (int) 9, 'bol' => (int) 4, 'bra' => (int) 4, 'can' => (int) 3, 'cansat' => (int) 3, 'chi' => (int) 2, 'cru' => (int) 3, 'car' => (int) 7, 'cbr' => (int) 1, 'ccan' => (int) 4, 'cde' => (int) 6, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 5, 'cla' => (int) 5, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 1, 'csa' => (int) 4, 'camsi' => (int) 7, 'dca' => (int) 4, 'din' => (int) 6, 'dzi' => (int) 7, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 15, 'fve' => (int) 3, 'gma' => (int) 13, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 8, 'han' => (int) 6, 'cav' => (int) 4, 'hma' => (int) 6, 'vpl' => (int) 2, 'sun' => (int) 4, 'lal' => (int) 7, 'lja' => (int) 7, 'lonja' => (int) 16, 'lsa' => (int) 5, 'mes' => (int) 7, 'mpo' => (int) 2, 'mbi' => (int) 12, 'mco' => (int) 1, 'mdo' => (int) 6, 'mtr' => (int) 5, 'cme' => (int) 7, 'egut' => (int) 8, 'ama' => (int) 6, 'nta' => (int) 6, 'nnu' => (int) 3, 'oeu' => (int) 6, 'osa' => (int) 3, 'pax' => (int) 8, 'pgr' => (int) 3, 'stu' => (int) 3, 'pvu' => (int) 6, 'ptr' => (int) 6, 'ppa' => (int) 4, 'pco' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 6, 'pso' => (int) 8, 'qlo' => (int) 7, 'rch' => (int) 5, 'rsi' => (int) 3, 'sbr' => (int) 4, 'sbo' => (int) 8, 'sci' => (int) 6, 'sed' => (int) 5, 'sgi' => (int) 7, 'sas' => (int) 5, 'smo' => (int) 2, 'sly' => (int) 3, 'spe' => (int) 3, 'spa' => (int) 3, 'tar' => (int) 12, 'tha' => (int) 4, 'tca' => (int) 5, 'esa' => (int) 3, 'tpr' => (int) 6, 'twi' => (int) 7, 'ugi' => (int) 5, 'vma' => (int) 6, 'vmu' => (int) 6, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb377300' $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